Class IlluminaPhasingMetrics


  • public class IlluminaPhasingMetrics
    extends htsjdk.samtools.metrics.MetricBase
    Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis. Phasing refers to the fraction of molecules that fall behind or jump ahead (prephasing) during a read cycle. For each lane/template read # (i.e. FIRST, SECOND) combination we will store the median values of both the phasing and prephasing values for every tile in that lane/template read pair.
    • Field Detail

      • LANE

        public long LANE
        Illumina flowcell lane number
      • TYPE_NAME

        public String TYPE_NAME
        Defines an Illumina template read number (first or second)
      • PHASING_APPLIED

        public double PHASING_APPLIED
        Median phasing value across all tiles in a lane, applied to the first and second template reads
      • PREPHASING_APPLIED

        public double PREPHASING_APPLIED
        Median pre-phasing value across all tiles in a lane, applied to the first and second template reads
    • Constructor Detail

      • IlluminaPhasingMetrics

        public IlluminaPhasingMetrics()
    • Method Detail

      • getPhasingMetricsForTiles

        public static Collection<IlluminaPhasingMetrics> getPhasingMetricsForTiles​(long lane,
                                                                                   Collection<Tile> tilesForLane,
                                                                                   boolean usePercentage)
        Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
      • getExtension

        public static String getExtension()
        This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.